Anticodon loop in tRNA

Anticoagulation systems in blood 634 Anticodon 231 Anticodon loop in tRNA... 

Each tRNA has a different sequence at the anticodon loop that is complementary to the codon sequence in the RNA. The recognition structure that is formed is analogous to double-stranded, antiparallel DNA. If the codon (in the RNA) is GCA (written 5 to 3 ), the anticodon loop in the tRNA would have the sequence UGC (again written to 5 to 3 )-... 

We know fhat the anticodon is a triplet of bases occupying the anticodon loop in the tRNA structure. By Watson-Crick base-pairing, this anticodon can recognize the... 

The ribosomal translocation process is quite complex. As the tRNAs move from A to P to E sites on the 16S RNA platform, the mRNA must also move in discrete single-codon steps. Tire acceptor stems of the tRNAs in the A and P sites must react at the appropriate times in the peptidyltransferase center. Study of protection from chemical probes suggests that tRNAs sometimes lie with the anticodon loop in the A site of the small ribosomal subunit, while the acceptor stem is in the P site of the large subunit (an A/P site as illustrated in Fig. 29-12B). Each aminoacyl-tRNA enters as a complex with EF-Tu and may initially bind with its anticodon in the A site and the acceptor stem with attached EF-Tu in a transient T site, the composite state being A/T. After loss of EF-Tu the acceptor stem can move into the A site to give an A/A state. The peptidyltransferase reaction itself necessarily involves movement at the acceptor stems by 0.1 nm or more. However, additional movement of 1 nm is needed to move the two tRNAs into states A/P and P/E, respectively. Movement of the mRNA then moves the... 

The D and t loops in tRNA interact with each other to form the tertiary structure, leaving only the anticodon with a single-stranded loop able to be cleaved by RNase. 

Figure 4.1 depicts the cloverleaf structure of a tRNA the bars represent base pairs in the stems. There are four arms and three loops - the acceptor, D, T pseudouridine C, and anticodon arms, and D, T pseudouridine C, and anticodon loops. Sometimes tRNA molecules have an extra or variable loop (shown in yellow in Fig. 4.1). The synthesis of transfer RNA proceeds in two steps. The body of the tRNA is transcribed from a tRNA gene. The acceptor stem is the same for all tRNA molecules and added after the synthesis of the main body. It is replaced often during lifetime of a tRNA molecule. The 3-D structure of a yeast tRNA molecule, which can code for the amino acid serine, shows how the molecule is folded with the...

Modification of the 2 -hydroxyl moiety on the ribose can also occur in the anticodon loop of tRNA. Although methylation of nucleosides is widespread, 2 -0-ribose methylation is found occasionally in the first position of the anticodon but not the second or third. Because the modification of nucleosides in and adjacent to the anticodon loop of tRNA is commonplace, Satoh et examined the decoding efficiency of tRNA in a cell-free expression system when either the first, second, or third nucleosides in the anticodon (either C-G-A or C-U-C) were methylated at the 2 -hydroxyl. While 2 -0-methylcytosine (Cm) in the first position increased the translational efficiency, methylation of both the second and third nucleoside (both the double modification as well as individual methylations at either position) resulted in dramatic reductions in activity. This study serves as a reminder that although methylation may seem simple and diverse throughout the RNA sequence, we still have much to learn about the functionality and biological importance of these modified nucleosides. 

Translation is accomplished by the anticodon loop of tRNA forming base pairs with the codon of mRNA in ribosomes Stop codons act to stop translation... 

U-Turn The U-tum is common at the apices of the anticodon loops of tRNAs and an invariant feature of their T / loops. The consensus sequence for U-tum is unpaired UNRN (N for any bases and R for any purines). In T / loops, U is replaced by pseudouridine. The turns which are stabilized by hydrogen bonds between imino proton of U(l) and a phosphate oxygen of R(3), and between 2 -OH of U(l) and N of R(3), introduce an abmpt 180° change in the backbone direction of larger loops. 

P. Auffinger, S. Louise-May, and E. Westhof, J. Chem. Soc., 117, 6720 (1995). Multiple Molecular Dynamics Simulations of the Anticodon Loop of tRNA in Aqueous Solution with Counterions. 

The estimated millisecond time scale for exchange cannot be due to a helix-to-coil transition because for hairpin loops lifetimes of 10- 1(X)/is are expected (no Mg + in 30 mAf Na" "). Robillard et al. (1977), Romer et al. (1970), and Coutts et al. (1975) have shown that disruption of the teritary structure is associated with a longer (2-23 ms) relaxation time. More recently, Labuda and Porschke (1980, 1982), using temperature-jump Y-base fluorescence relaxation kinetics, have identihed a conformational transition in the anticodon loop of tRNA in a similar Mg + buffer. Their measured relaxation time of 1 ms at 7°C is, however, shorter than our rate process. 

The anticodon region consists of seven nucleotides, and it recognizes the three-letter codon in mRNA (Figure 38-2). The sequence read from the 3 to 5 direction in that anticodon loop consists of a variable base-modified purine-XYZ-pyrimidine-pyrimidine-5h Note that this direction of reading the anticodon is 3 " to 5 whereas the genetic code in Table 38—1 is read 5 to 3 since the codon and the anticodon loop of the mRNA and tRNA molecules, respectively, are antipar-allel in their complementarity just like all other inter-molecular interactions between nucleic acid strands. 

There are 64 different three-letter codons, but we don t have to have 64 different tRNA molecules. Some of the anticodon loops of some of the tRNAs can recognize (bind to) more than one condon in the mRNA. The anticodon loops of the various tRNAs may also contain modified bases that can read (pair with) multiple normal bases in the RNA. This turns out to be the reason for the wobble hypothesis, in which the first two letters of a codon are more significant than the last letter. Look in a codon table and you ll see that changing the last base in a codon often doesn t change the identity of the amino acid. A tRNA that could recognize any base in codon position 3 would translate all four codons as the same amino acid. If you ve actually bothered to look over a codon table, you realize that it s not quite so simple. Some amino acids have single codons (such as AUG for Met), some amino acids have only two codons, and some have four. 

How, in turn, does the synthetase recognize its specific tRNA From extensive mutagenesis studies, it appears that the aminoacyl-tRNA synthetases recognize particular regions of the tRNA molecule, most often in their anticodon loops and/or in their acceptor stems. 

Figure 10 Alteration of the genetic code for incorporation of non-natural amino acids, (a) In nonsense suppression, the stop codon UAG is decoded by a non-natural tRNA with the anticodon CUA. In vivo decoding of the UAG codon by this tRNA is in competition with termination of protein synthesis by release factor 1 (RFl). Purified in vitro translation systems allow omission of RF1 from the reaction mixture, (b) A new codon-anticodon pair can be created using four-base codons such as GGGU. Crystal structures of these codon-anticodon complexes in the ribosomal decoding center revealed that the C in the third anticodon position interacts with both the third and fourth codon position (purple line) while the extra A in the anticodon loop does not contact the codon.(c) Non-natural base pairs also allow creation of new codon-anticodon pairs. Shown here is the interaction of the base Y with either base X or (hydrogen bonds are indicated by red dashes).

Many specificity elements for tRNA are also the result of interactions with the three bases of the anticodon loop C34 (and U34), U35, and G36 are each bound within separate pockets of the anticodon-binding domain." Although it is likely that in free tRNA , like most other free tRNAs, anticodon bases are normally stacked with one another, binding by GlnRS disrupts this base stacking, allowing each base to be recognized by... 

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